Package: EventPointer
Type: Package
Title: An effective identification of alternative splicing events
	   using junction arrays and RNA-Seq data
Version: 3.19.0
Authors@R: c(person("Juan Pablo","Romero",role=c("aut"),email = "jpromero@ceit.es"),
  person("Juan A.", "Ferrer-Bonsoms",role=c("aut","cre"),email = "jafhernandez@tecnun.es"),
  person("Pablo", "Sacristan",role=c("aut"),email = "a904719@alumni.unav.es"),
  person("Ander", "Muniategui",role=c("aut")),
  person("Fernando", "Carazo",role=c("aut")),
  person("Ander", "Aramburu",role=c("aut")),
  person("Angel", "Rubio",role=c("aut"),email = "arubio@tecnun.es")
    )
Description: EventPointer is an R package to identify alternative splicing events 
		that involve either simple (case-control experiment) or complex experimental designs 
		such as time course experiments and studies including paired-samples. The algorithm can
		be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq).
        In the latter, EventPointer can work with annotated splicing events or can build 
        a splicing graph from the RNA-Seq reads and then identify new and specific 
        alternative splicing events. 
		The software returns a data.frame with the detected alternative splicing 
		events: gene name, type of event (cassette, alternative 3',...,etc), genomic 
		position, statistical significance and increment of the percent spliced in (Delta PSI) for all 
		the events.
		The algorithm can generate a series of files to visualize the detected alternative 
		splicing events in IGV. This eases the interpretation of results and the design 
		of primers for standard PCR validation.
Depends:
    R (>= 3.4),
    SGSeq,
    Matrix,
    SummarizedExperiment
Imports:
    txdbmaker,
    stringr,
    GenomeInfoDb,
    igraph,
    MASS,
    nnls,
    limma,
    matrixStats,
    RBGL,
    prodlim,
    graph,
    methods,
    utils,
    stats,
    doParallel,
    foreach,
    affxparser,
    GenomicRanges,
    S4Vectors,
	IRanges,
	qvalue,
	cobs,
	rhdf5,
	BSgenome,
	Biostrings,
	glmnet,
	abind,
	iterators,
	lpSolve,
	poibin,
	speedglm,
	tximport,
	fgsea
Suggests:
    knitr,
    rmarkdown,
    BiocStyle,
    RUnit,
    BiocGenerics,
	dplyr,
	kableExtra
License: Artistic-2.0
LazyData: true
RoxygenNote: 7.3.3
Encoding: UTF-8
biocViews: AlternativeSplicing, DifferentialSplicing, mRNAMicroarray, RNASeq, Transcription, Sequencing, TimeCourse, ImmunoOncology
VignetteBuilder: knitr
Url: https://github.com/jpromeror/EventPointer
BugReports: https://github.com/jpromeror/EventPointer/issues
git_url: https://git.bioconductor.org/packages/EventPointer
git_branch: devel
git_last_commit: b63b3a9
git_last_commit_date: 2025-12-16
Repository: Bioconductor 3.23
